Reduced Representation Bisulphite Sequencing on FACS purified cell subpopulations of human prostate cancers and normal tissues.

Prostate adenocarcinomas contain a predominance of cells with luminal features that display aberrant DNA methylation patterns with useful diagnostic and prognostic potential. However, the DNA methylation features of basal and luminal cells in both normal and cancer tissues remain largely unknown. We have generated genome-wide DNA methylation profiles for FACS purified basal and luminal prostate tumour cells, obtained from radical prostatectomy samples and their paired normal counterparts isolated from unaffected regions in the same patient’s gland. Matched tumour-directed (cancer) and contralateral (normal) core needle biopsies, obtained from 4 treatment-naïve prostate cancer patients undergoing radical prostatectomies, were enzymatically dissociated and FACS sorted into EpCAM+CD49f-CD24+ (luminal) and EpCAM+CD49f+CD24- (basal) cell populations at >95% purity. For convenience, we named these supbopulations as follows. CL: EpCAM+CD49f-CD24+ cells purified from tumor-directed biopsies; CB: EpCAM+CD49f+CD24- cells purified from tumour-directed biopsies; NL: EpCAM+CD49f-CD24+ cells from contralateral biopsies; NB: EpCAM+CD49f+CD24- cells purified from contralateral biopsies. This yielded 4 CL and CB populations, and 3 matched NL and NB populations (in one prostate the palpable tumour was extended to most of the prostate and it was not possible to obtain a contralateral biopsy). DNA obtained from each of these isolates was then subjected to Reduced Representation Bisulphite Sequencing (RRBS). --------------------- *Raw data is not available due to privacy concerns. Thus, this dataset is incomplete.*